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Cluster the synteny network using the Infomap algorithm

Source: R/05_phylogenomic_profiling.R
cluster_network.Rd

Cluster the synteny network using the Infomap algorithm

Usage

cluster_network(
  network = NULL,
  clust_function = igraph::cluster_infomap,
  clust_params = NULL
)

Arguments

network

A network represented as an edge list, which is a 2-column data frame with node 1 in the first column and node 2 in the second column. In a synteny network, node 1 and node are the anchor pairs.

clust_function

Function to be used to cluster the network. It must be one the functions from the cluster_* family in the igraph package (e.g., cluster_infomap, cluster_leiden, etc). Default: igraph::cluster_infomap.

clust_params

A list with additional parameters (if any) to be passed to the igraph clustering function. Default: NULL (no additional parameters).

Value

A 2-column data frame with the following variables:

Gene

Gene ID.

Cluster

Cluster ID as identified by infomap.

Examples

data(network)
clusters <- cluster_network(network[1:500, ])